The following error appears on all my Piwik installations when using the automatic upgrade function. After that, all installations seem to work normal.

There is an error. Please report the message and full backtrace in the Piwik forums.
Notice: Undefined property: Piwik_CoreUpdater_Controller::$pathRootExtractedPiwik in /srv/www/piwik/plugins/CoreUpdater/Controller.php on line 99